Aldon Smith, who seemed to be getting beyond the alcohol-related trouble that plagued him the last three seasons, was arrested in Santa Clara on Thursday for suspicion of DUI, hit and run and vandalism, according to Santa Clara police.

He was booked into the Santa Clara County main jail, where bail was set at $26,000. He left the jail at around 8:30 a.m., telling KTVU, “It wasn’t a DUI … the truth will come out.”

Thursday was the first day off for the 49ers since training camp opened July 31.

This is the fifth time Smith, 25, has been arrested or charged with a crime since January 2012, a DUI arrest in Miami Beach. He also was arrested for DUI in September 2013, an incident that led to him leaving for an alcohol rehabilitation program for five weeks. He was suspended nine games last season for his various incidents.

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Smith had not been in trouble since an April 2013 incident at LAX airport, and on Tuesday general manager Trent Baalke said the 49ers were interested in re-signing Smith at some point. No charges were filed in the LAX incident in which Smith was arrested for making a bomb threat.

“Aldon’s like any young player, he’s growing up, he’s maturing,” Baalke said. “You see that with a lot of these guys. Some of them get themselves in a few more situations that you wish they didn’t. If you asked them, I think they’d say the same thing. Really pleased with the way he’s handled things, the way he’s working both personally and professionally.”

That extension now seems unlikely, and Smith’s spot on the team also is in question.

In December, the 49ers terminated Ray McDonald’s contract after the long-time defensive end was named in a police investigation for the second time in three months. Baalke and CEO Jed York said “a pattern of poor decision making” led to McDonald’s release and that “multiple distractions for this organization and this football team that really can no longer be tolerated.”

The 49ers picked up the fifth-year option on Smith’s contract last season, although there was internal disagreement initially on whether that was wise someone who has been in so much trouble. Smith and the 49ers restructured that contract in March so his $9.75 million deal would be paid incrementally throughout the season rather than fully guaranteed.

If the 49ers release Smith, they would have a $1.6 million hit against their salary cap, according to Spotrac.com

The 49ers consider Smith their best pass rusher, and he had 42 sacks in his first 43 games.

Third-round draft pick Eli Harold has been lining up behind Smith at right defensive end. Aaron Lynch, Corey Lemonier and Marcus Rush are the other backup outside linebackers on the offseason roster. It’s possible starter Ahmad Brooks would move from the left to the right side and that Lynch would play on the left.

Smith’s nine-game suspension last year was related to the 2013 DUI arrest and gun possession charges stemming from an out-of-control party at Smith’s unincorporated Santa Clara County home in 2012. When he returned to the 49ers, he was asked if he had turned his life around.

“I’d say, honestly, time will show,” he said. “I’m not going to sit here and give you some, whatever, crazy answer. Time will show, you know.”

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